Commits for angie

v265_base to v266_preview (2012-03-27 to 2012-04-10) v266

• Feature #6152 (Variant Annotation Tool): instead of having a callercreate the sql connection outside of annoStreamDb, and have to remember not to share it, just allocate the connection inside annoStreamDb. This introduces a dependency on hdb, but I guess that's inevitable. :)
  • src/hg/inc/annoStreamDb.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/annoStreamDb.c - lines changed 14, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTester.c - lines changed 9, context: html, text, full: html, text
• Comment tweak.
  • src/inc/annoStreamer.h - lines changed 1, context: html, text, full: html, text
  • src/lib/annoStreamer.c - lines changed 1, context: html, text, full: html, text
• bugfix for #6152: was skipping the bin column twice, oops.
  • src/hg/lib/annoStreamDb.c - lines changed 3, context: html, text, full: html, text
• Feature #6152 (Variant Annotation Tool): Added annoStreamWig and annoGrateWig,which led to some significant changes: annoRow is now polymorphic (words[] vs. wig float[]), annoFilter has a new function to apply filter(s) to a single number, and annoFormatTab can print out per-base wiggle values or average wiggle values (hardcoded to do per-base until a real config option is added). One puny test case was verified against mysql & table browser output.
  • src/hg/inc/annoGrateWig.h - lines changed 11, context: html, text, full: html, text
  • src/hg/inc/annoStreamWig.h - lines changed 11, context: html, text, full: html, text
  • src/hg/inc/wiggle.h - lines changed 19, context: html, text, full: html, text
  • src/hg/lib/annoGrateWig.c - lines changed 78, context: html, text, full: html, text
  • src/hg/lib/annoStreamWig.c - lines changed 152, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTester.c - lines changed 74, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTests.mk - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/snpConsDbToTabOutShort.txt - lines changed 39, context: html, text, full: html, text
  • src/inc/annoFilter.h - lines changed 5, context: html, text, full: html, text
  • src/inc/annoRow.h - lines changed 16, context: html, text, full: html, text
  • src/lib/annoFilter.c - lines changed 29, context: html, text, full: html, text
  • src/lib/annoFormatTab.c - lines changed 81, context: html, text, full: html, text
  • src/lib/annoGratorQuery.c - lines changed 1, context: html, text, full: html, text
  • src/lib/annoRow.c - lines changed 57, context: html, text, full: html, text
• lineFileTabixMayOpen: initialize lf->tabixIter to ti_iter_first sowe can start reading lines from the beginning of the tabix-indexed file, without having to make an iterator for a specific region.
  • src/lib/linefile.c - lines changed 1, context: html, text, full: html, text
• Feature #6152 (Variant Annotation Tool): Added annoStreamVcf, whichled to yet more significant changes to annoRow: instead of every row declaring its type and annoRow{Free,Clone} taking a numCols argument that is meaningless for wig, now annoRow{Free,Clone} take the row's source annoStreamer as an argument. The annoStreamer now has public members (rowType and numCols) that provide all information needed about the row. annoStreamer constructors need to set rowType.
  • src/hg/lib/annoGrateWig.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/annoStreamDb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/annoStreamWig.c - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTester.c - lines changed 90, context: html, text, full: html, text
  • src/hg/lib/tests/annoGratorTests.mk - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/vcfEx1.txt - lines changed 110, context: html, text, full: html, text
  • src/hg/lib/tests/expected/annoGrator/vcfEx2.txt - lines changed 120, context: html, text, full: html, text
  • src/inc/annoGrator.h - lines changed 1, context: html, text, full: html, text
  • src/inc/annoRow.h - lines changed 8, context: html, text, full: html, text
  • src/inc/annoStreamVcf.h - lines changed 12, context: html, text, full: html, text
  • src/inc/annoStreamer.h - lines changed 4, context: html, text, full: html, text
  • src/inc/vcf.h - lines changed 17, context: html, text, full: html, text
  • src/lib/annoFormatTab.c - lines changed 10, context: html, text, full: html, text
  • src/lib/annoGrator.c - lines changed 7, context: html, text, full: html, text
  • src/lib/annoGratorQuery.c - lines changed 3, context: html, text, full: html, text
  • src/lib/annoRow.c - lines changed 16, context: html, text, full: html, text
  • src/lib/annoStreamVcf.c - lines changed 135, context: html, text, full: html, text
  • src/lib/annoStreamer.c - lines changed 1, context: html, text, full: html, text
  • src/lib/makefile - lines changed 1, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 60, context: html, text, full: html, text
• Merge branch 'annoGratorWigVcf'
• Fixing style errors found by Brian in code review: public methodsdefined in structs are functions, so the comment should go below the definition not above.
  • src/inc/annoFormatter.h - lines changed 14, context: html, text, full: html, text
  • src/inc/annoGrator.h - lines changed 5, context: html, text, full: html, text
  • src/inc/annoStreamer.h - lines changed 17, context: html, text, full: html, text
• Track #1656 (GWAS Catalog): bi-monthly update.
  • src/hg/makeDb/doc/hg18.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 4, context: html, text, full: html, text